SMTL ID : 4gsz.2 (1 other biounit)

Crystal Structure of the Zn2+5-Human Arginase I-ABH Complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.101, D.124, D.128, D.232 Ligands: ZN.2, ABH.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.101, A:D.124, A:D.128, A:D.232 ZN.2: 7 residues within 4Å: Chain A: D.124, A.125, H.126, D.232, D.234 Ligands: ZN.1, ABH.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.124, A:H.126, A:D.232, A:D.234, A:D.234 ZN.4: 3 residues within 4Å: Chain A: H.141, E.277 Ligands: ABH.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.141, A:E.277, A:E.277, H2O.2 ZN.5: 2 residues within 4Å: Chain A: H.115, D.117 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.115, A:D.117, H2O.2 ZN.6: 6 residues within 4Å: Chain B: H.101, D.124, D.128, D.232 Ligands: ZN.7, ABH.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.101, B:D.124, B:D.128, B:D.232 ZN.7: 7 residues within 4Å: Chain B: D.124, A.125, H.126, D.232, D.234 Ligands: ZN.6, ABH.8 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.124, B:H.126, B:D.232, B:D.234, B:D.234 ZN.9: 3 residues within 4Å: Chain B: H.141, E.277 Ligands: ABH.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.141, B:E.277, B:E.277, H2O.4 ZN.10: 2 residues within 4Å: Chain B: H.115, D.117 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.115, B:D.117, H2O.4 ZN.11: 6 residues within 4Å: Chain C: H.101, D.124, D.128, D.232 Ligands: ZN.12, ABH.13 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.101, C:D.124, C:D.128, C:D.232 ZN.12: 7 residues within 4Å: Chain C: D.124, A.125, H.126, D.232, D.234 Ligands: ZN.11, ABH.13 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.124, C:H.126, C:D.232, C:D.234, C:D.234 ZN.14: 3 residues within 4Å: Chain C: H.141, E.277 Ligands: ABH.13 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.141, C:E.277, C:E.277, H2O.5 ZN.15: 2 residues within 4Å: Chain C: H.115, D.117 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.115, C:D.117, H2O.6

3 x ABH: 2(S)-AMINO-6-BORONOHEXANOIC ACID(Non-covalent)

ABH.3: 17 residues within 4Å: Chain A: H.101, D.124, H.126, D.128, N.130, S.137, H.141, G.142, D.183, E.186, D.232, D.234, T.246, E.277 Ligands: ZN.1, ZN.2, ZN.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.130, A:S.137, A:H.141, A:D.183, A:T.246 Water bridges: A:T.135, A:T.135, A:N.139 ABH.8: 17 residues within 4Å: Chain B: H.101, D.124, H.126, D.128, N.130, S.137, H.141, G.142, D.183, E.186, D.232, D.234, T.246, E.277 Ligands: ZN.6, ZN.7, ZN.9 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.130, B:S.137, B:H.141, B:D.183, B:T.246 Water bridges: B:T.135, B:T.135, B:N.139 ABH.13: 17 residues within 4Å: Chain C: H.101, D.124, H.126, D.128, N.130, S.137, H.141, G.142, D.183, E.186, D.232, D.234, T.246, E.277 Ligands: ZN.11, ZN.12, ZN.14 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.130, C:S.137, C:H.141, C:D.183, C:T.246 Water bridges: C:T.135, C:T.135, C:N.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

D'Antonio, E.L. et al., Structure and function of non-native metal clusters in human arginase I. Biochemistry (2012)

Release Date

2012-09-26

Peptides

Arginase-1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

Arginase-1

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